Doctor Glee
by wherethepeopleare
Summary: What happens when McKinley is under alien attack? What happens when a man in a blue box arrives? What happens when someone takes a shine to the man in the bow tie? The 11th doctor, all th glee characters, massive adventure.
1. Chapter 1

**Doctor Glee-A Strange Inspector**

"Doctor, where the hell are we going?" the red haired girl yelled over the top of the Tardis' wailing sirens

"Somewhere that's in danger, not quite sure where yet, ahh!" the bow-tie wearing doctor franticly pushed buttons and flicked switches, gripping onto the bars when the machine jolted.

"Oh that's reassuring!" Amy remained with her hands firmly gripped on the metal bar by the door; letting the doctor do all the time lord work.

The machine stopped with a thud. Both of them fell to the floor, the Doctor was quick on his feet.

"Come on then Amy, chop chop, tally-ho, pip pip on your feet!" the smooth man swung open the doors to reveal a surprisingly dim setting, not what you'd expect a place in danger to look like. Amy clambered off the floor and left the blue box.

"Well, this looks exciting! Outside a crumby high school!" she put her hands in her pockets and sighed.

"Don't knock it before you try it, like Marmite, lets go," The Doctor strode towards the entrance to the school, followed by a reluctant Amy.

The pair were met with a nervous looking man at the entrance.

"Oh hello, you must be the inspectors," the man spoke with an accent; the pair assumed he was the Principal.

"Inspectors? Yes! The inspectors of course, I'm John Smith nice to meet you," he shook the shaky man's hand, "and this is my assistant, Angela May, can we please see where the students are?" The doctor spoke confidently and pretty quick, Amy smiled and nodded along with the charade.

"Yes, well, you are a bit late, lessons have finished but the schools glee club is rehearsing now if you would like to go there," the principal lead The Doctor and Amy towards the choir room, where a group of young teens were sitting down singing 'I want to break free'.

"William, can I speak to you for a moment?" the principal shouted over the noise and Will stopped the singing.

He took Will to one side, while the doctor scanned the room with his eyes.

"I have to go to a meeting, William, but these are the school board inspectors I was telling you about, let them sit in for a while and make a good impression, please!" Will nodded, the principal left the room.

"Guys, um these people are from the school board, so if you just, sing well, and oh, would you like to hear them sing something?" will laughed nervously.

"No, not really, what I really need to do is talk, we can sing another time but not now," He pulled up a chair and sat directly in front of the teens, one of which, a brunette looked extremely offended and the Doctors refusal.

"Hi, I'm the Doctor and you need to be completely honest with me, ok?"

The offended girl shot up her hand.

"Yes, um you, girl in the rainbow jumper,"

"Excuse me, but this is our glee club rehearsal, and if you don't mind we have Nationals in a couple of weeks so we really need to practise," the girl flashed a stage school smile, and sat upright.

"You, what's your name?" the Doctor narrowed his eyes.

"Rachel Berry,"

"Rachel, I can tell you're really serious about singing, and why wouldn't you be? I love it myself, had lunch with Mozart, lovely man. But Rachel, this is more important than learning scales or working out harmonies, this is so much more important, so if you wouldn't mind," the Doctor was serious, he had received a message on the physic paper before they arrived telling him that this school was in grave danger, he needed to find out why.

Rachel looked shocked, Will broke the silence,

"Um, Doctor? If you don't mind me asking, what is this about, I thought you were from the school board,"

"Yeah…about that, I'm kind of not," he turned back to the glee club, "I need to ask a few questions."

Amy took a seat next to a gothic looking girl and listened to the Doctor.

"Ok, has anything, out of the ordinary happened lately, anything a bit different, a bit weird?" the group shuffled a little in their seats, a blonde girl raised her hand.

"Um, I think my fish is pregnant, he's called Harvey,"

"Really Brittany?" the gothic girl questioned.

"No, I'm thinking more really strange things…anything?"

A tall boy raised his hand, "Um, something happened yesterday,"

The doctor rose to his feet and walked over to the brown haired boy, "Go on," he ushered.

"Well, I was in the locker room after football practice, everyone else had gone home so it was just me, and I saw a shadow against the other locker, and I know it wasn't me. And I also heard this haunting singing noise, it was all kinds of creepy."

"What's your name?" the doctor questioned, almost immediately.

"Finn."

"Finn, what did the shadow look like?"

"I don't know, long, flowy, like a ghost I guess," Finn was beginning to feel a little intimidated by the man looming over him with a serious expression on his face.

"Great, ok, in the locker room you say," and without so much as a goodbye, the man in the bow tie swiftly left the room.

"Sorry about that, he does that a lot," Ay assured the group.

"What's your name?" a blonde boy asked.

"Amy,"

"Your friends weird, Amy," a fashionable boy said, "and you need to talk to him about that bow tie, not a good look."

"Hey bow ties are cool," the Doctor returned, sonic screwdriver in hand, and began scanning the room.

"What the hell is he doing?" a diva-like girl raised her eyebrow at the man.

"Scanning the place, it's just what he does, what's your name?" she stuck her hand out to the girl.

"Mercedes," she shook it and smiled.

"I'm Kurt," the fashionable boy who was against bow ties, stuck out his hand effeminately, which Amy shook, "This is my boyfriend, Blaine."

"Nice to meet you."

"You! What's you're name?" the Doctor stopped scanning and pointed to a boy in a wheelchair.

"Artie."

"Artie, how long have you been in that wheelchair?" the Doctor leant over him, disregarding all personal space rights.

"About eight years,"

"Damn!" the Doctor walked away and continued scanning.

"Why damn?" Artie looked confused.

"Because, I'm getting a strong signal of wyndochlostopip, which is basically something that is emitted into the air via a failed body part, e.g. your legs, but the thing is it only starts to emit after 14 years of failure so it can't possibly you so I'm back to being confused again!"

"This guy is crazy," Mercedes widened her eyes, genuinely stunned at what was coming out of this man's mouth.

"What do you think it is Doctor?" Amy asked as the man scanned a white board rubber.

"No idea, but when I went in the locker room I heard the same singing Fann was describing,"

"Finn," the tall boy corrected him.

"Oh yeah, Finn, anyway, I scanned the lockers and there's definitely something there and it's only a matter of time before it makes its presence known."

"Ok, what the hell is going on, what are you talking about, who the hell are you?" Kurt stood up creating silence in the room, the Doctor walked towards him.

"I'm the Doctor,"

"You can't just say you're a doctor, a doctor of what? What's your real name?" Kurt was getting more and more frustrated.

"Just call me the Doctor,"

"Oh my God, how are we supposed to trust you when you won't even tell us you're real name?"

"Because right now, you need to trust me. You don't need to know my name to know that you could all die soon, and you need to let me do what I need to do to stop that from happening, ok, Kurt?" The room fell dead silent, Kurt returned to his seat, stunned. Mr. Schue became the voice of reason.

"Excuse me, you can't just walk in here and tell these kids there gonna die, who the hell do you think you are?" Will questioned, only inches away from the Doctor's face.

The Doctor grinned.

"I'm the Doctor."

**Tell me what you think, should I continue? **

**Thanks **

**x**


	2. Chapter 2

**Doctor Glee**

"I don't want to die," Brittany clung onto the arm rest of Artie's chair.

"And you won't, as long as you do what I say, now first of all I-," the Doctor was interrupted by a loud bang above their heads. The group looked up with fear.

"Okay, no one panic, Amy come with me, we're gonna go upstairs and see what that was," The Doctor's eyes never stopped glaring upwards, he beckoned Amy towards the door and the pair exited swiftly.

"Doctor what was that," Amy panted, as she ran along side the Doctor.

"If I knew would I be running this fast?"

The Pair scrambled up flight of stairs and were faced with two doors, one lead to a brightly lit staff room, the other to a dark janitors closet.

"Which one, Doctor?" Amy questioned, catching her breath.

"Which one do you think? The scariest looking one, of course," he flung open the door and crept inside.

"Of course," she repeated.

The janitor's closet was a lot bigger than anticipated; obviously janitors need a lot of storage. The bulb was gone so the only light was emitted from the Doctors screwdriver. Its familiar buzz was the only sound.

"Anything?" Amy questioned, looking in various boxes and behind brooms.

"No, just a vile smell, Amy was that you?" he sniffed, pulling a face.

"Doctor! No! Was it you?"

"Don't be ridiculous, I wouldn't even entertain the idea," the buzzing stopped, so did the light.

"Doctor, turn it back on,"

"I would if I could," The Doctor tapped the metal device on his palm but to no avail.

The pair stopped dead still as a new sound filled the room, the sound of singing. It was haunting.

"What the hell is that?" she whispered.

"Shhh!" the Doctor walked further into the darkness, the sound got louder.

"Hey!" a voice came from the door, making the pair jump.

"Ahh! What was that? Oh, Hi Rachel is it?" The Doctor turned towards the open door and the smiling girl standing in it, "Can we help you?"

"Actually I was wondering if I could help you, you see I'm very good at solving mysteries, when I was younger and I played Scooby Doo, I was always Daphne, another girl called Stephanie wanted to be her but I had to let her know that even though she had the matching headband and dress, my talent simply outshone hers and I was better suited for that particular role in that particular playground game. Anyway, I was very good at it and I could always tell whether it was the butler or the janitor under the mask so I was just wondering if you want help in your weird Doctor business," Rachel finished with a smile on her face, leaving the Doctor and Amy speechless.

"Wow, you talk fast," The man in the bowtie walked forward with a smile, "Rachel, um that's really great but the thing is, I really don't need-,"

The door slammed shut, Rachel screamed, "What was that?"

The Doctor ran to the closed door and tried to open it, he failed miserably.

"Why won't it open?" Amy joined in the desperate struggle to open the door.

"I don't know," The Doctor pulled at the handle but eventually admitted defeat.

"Wait, how the hell did that door just slam shut by itself, that's not possible," Rachel's voice remained at its usual fast pace.

"Doesn't seem possible, does it?" the Doctor questioned.

"But it's pretty normal for us," Amy assured, pacing back and forth.

"We're trapped now, aren't we?" Rachel guessed.

"Correct." The Doctor began to scan again.

"Oh my God, what is that smell, was that you?" Rachel asked the man scanning the room.

"No! Honestly I don't know why I seem the type to do that," the offended Doctor scanned the door handle.

The singing began again. No real words were sung, just a continuous melody.

The group stood dead still and looked around them.

"Wha-," Rachel began, but was quickly shut off by a shushing Doctor.

The chilling sound stopped, Amy let out a breath she was holding.

"Interesting," the Doctor narrowed his eyes and strode towards the door.

"Come on!" The man pleaded as he tried once again to pry open the door.

"Why don't you use your flash-lighty thingy," Rachel waved her arms towards the supposed 'flash light.'

"First of all it's a screw driver and secondly, don't you think I've already tried that?"

"Just trying to help," Rachel mumbled and was unheard by the Doctor.

"Doctor what are you doing?" Amy yelled as the man started climbing up the unstable shelves towards the ceiling, screwdriver in his mouth.

"um hying hoo het updar do da ventx," the doctor attempted to speak.

"What?" the girls cried in unison.

Reluctantly, the man in the bow tie adjusted his hands and removed the sonic device from his mouth.

"I'm trying to get up there to the vents," he informed, returning the screwdriver to its original position he continued to climb.

"Oh," the girls chorused.

Reaching the top of the shelves he began reaching around for the door to said vent.

"Aha!" he triumphed, pulling himself up into the mysterious darkness.

"Where'd he go?" Rachel asked.

"Doctor?" Amy called to the ceiling, only to see a smiling face emerge.

"Are you coming then?" he asked, with a sense of adventure in his voice.

* * *

><p>"Doctor, this is really scary," Rachel confessed as the newly formed trio crawled through the narrow metal maze.<p>

"No, there's nothing scary about this, you try sitting through an entire Shakespeare play on the front row when the lead is dangerously overweight and dangerously close to the edge," he assured, keeping his eyes forward and pushing back his fallen fringe.

"You're so weird," Rachel continued to crawl through the darkness, in between the time travellers, adjusting her skirt every so often.

"Oh hey, my screwdriver," he smiled as the sonic device began to light up again once more, "Nice."

The three crawled for another 2 minutes until the Doctor stumbled across a metal grid.

"Okay, looks like this is the top of the choir room," he declared, looking down through the metal bars to see the New Directions sitting in their usual formation.

"Wow, it looks different from a birds eye view, oh I can see down Blaine's shirt!" Rachel pointed out.

"Really?" Amy perked up, pushing the doctor out the way to get a better view.

"Honestly Amy," the man scanned the bars and tutted, "Look out!" he yelled down to the glee club just as the bars fell to the ground, making all the girls jump and scream.

"Sorry!" he held up his hand and jumped down, brushing his suit off when he landed. The two girls followed. Kurt fanned himself, trying to recover from the shock.

"How the hell did you? Where did you? What? How the hell did you get in the vents?" Will spluttered out.

"Long story, trapped in a janitors closet, sorry about the ceiling," he looked up and winced, "Yeah, that's a big hole, anyway I need a drink don't you?"

* * *

><p>"So, wait, let me get this straight, you're a time, lord is it?" Quinn questioned as she sat with the rest of the group in the abandoned canteen.<p>

"Time lord, yep," the Doctor confirmed, sipping a slushy.

"And, you have a time machine, called a Tardis?" the blonde continued, looked confused.

"What does that stand for, Totally Annoying Retarded Dude in Space?" Puck mocked, receiving a high five from Sam.

"Shut up, Puckerman," Rachel hissed from across the table.

"Well, he's partly right, it actually stands for, Time and Relative Dimension in Space," the Doctor smirked.

"I'm so confused," Brittany confessed.

"Wait, guys do you hear that?" Mercedes interrupted.

The singing began again, this time accompanied with loud banging. Mr Schue immediately took the protective role and stood up, ready to defend his glee club.

The loud noise increased, and got faster.

The group slowly backed away from the door.

The melody became more intense, until suddenly a remarkably high pitched note was belted out, ringing around the room.

A sudden wave of pain swept over the large group, who all fell to the floor, clinging to their chests, the doctor included. Everyone was wincing in pain.

The singing stopped, leaving the newly formed gang in a heap on the canteen floor.

**To be continued…..**


	3. Chapter 3

**Doctor Glee**

Amy's eyes were first to fly open. She found herself lying half on top of a boy who's name she had picked up to be 'Puckerman'. She quickly sat up and looked around her at the group of unconscious teens, she began to remember how this happened. She remembered the pain in her chest, in her heart. She figured that everyone experienced this same feeling.

"Doctor?" she crawled to the man who was lying with his arms out, "Doctor, can you hear me?" she shook his shoulders.

"Is he ok?" she heard a voice ask behind her, the question came from Quinn, who was slowly sitting up and holding her head.

Amy ignored the girl and continued to smack the Doctor's face, hoping for a reaction.

One by one the glee club regained consciousness, until only the Doctor remained.

"What the hell happened?" Finn asked.

"I remember feeling a really sharp pain in my chest and then just falling to the ground," Blaine recalled, pulling himself from the cold, canteen floor.

"Me too," Mercedes added.

The rest of the group nodded as they began to recall the events.

"Is everyone ok, guys?" Mr Schue asked, checking everyone was still there.

"No! Can't you see? The Doctor won't wake up!" Amy yelled, still kneeling by the man's side.

"Oh my God, splash some water on his face or something," Tina suggested, clinging onto Mike.

"No way Tina, that's such a stupid idea, just keep smacking him," Santana hissed.

"AH!" The man on the floor sprung up with a yell that made all of the girls scream with shock.

"Wow! That was strange, ah, still alive I see, great," he examined himself, "Yep, still the same, everyone ok? Good," Amy sighed with relief as the Doctor stood to his feet.

"Are you ok?" Amy held him by the shoulders.

"Course I am, I'm not ginger, that's a good thing," he said, leaving her grasp, Amy scowled.

"Doctor, what the hell was that, all our chests started hurting then we blacked out," Mercedes questioned, taking a step closer to the man in the bowtie.

"I don't know," the Doctor confessed.

"Why did it affect all of us?" Blaine stepped in.

"I don't know,"

"Where did that singing come from?" asked Mike.

"I don't know,"

"Oh my God, what do you know?" a frustrated Quinn blurted out, hands on her hips.

"Lots of things! But come on give me a break, I've just woken up from an alien induced coma, I'm not going to know all the answers straight away now am I?" he grinned, then turned towards the door, Amy quickly followed.

"Wait, can I come?" Rachel skipped towards the pair.

"Um, sure, we could do with an extra pair of hands, besides if I said know you'd only give me some sob story about a school production or a wrong note you did in a performance that sent you into a flurry of tears, so sure," the three headed towards the door.

"Hey, if she gets to go, then I wanna go to!" Kurt raised his hand.

"And me!" Added Finn, which resulted in a chorus of angry teenagers wanting to see what's going on in their school.

"Guys, guys, come on, calm down!" Will stepped in front of his tudents and waved his arms to be noticed, "Now if anyone's gonna go with the Doctor, it should be a responsible adult," he turned to a stunned Doctor and smiled, "Right?"

"Right sure, whatever, can we go now please?" he pointed to the door.

"Aw hell to the no Mr Schue, if there's something goin' on in our school, we have the right to know about it!" Mercedes' argument received a chorus of 'Yeah!'s and 'That's right!'s from therest of the group.

The Doctor sighed.

* * *

><p>"And this, is the Tardis," the Doctor flung open the doors to allow the large group of his new companions to walk inside.<p>

"Oh my," Kurt gasped.

"What the," Puck walked outside again, and circled the blue box, "It's,"

"Bigger on the inside, uh-huh," Amy finished, walking up the stairs to the Doctor, who had given in on the idea of everyone following him, including Mr Schue.

"This is so weird," Tina exclaimed.

"Oh my," Kurt repeated, lost for words.

"How can it be this big it's just a tiny blue box?" Santana was the first to walk up towards the center, questioning the Doctor.

"Clever isn't it?" he jeered.

"Am I being punked?" Sam looked around.

"Punk, a sort of gothic slash rocker type person yes?" The Doctor asked, confused.

"You're so weird," Sam muttered.

"Anyway, welcome to my Tardis, make yourself at home, blah blah blah, actually no, don't make yourself at home, God knows what you humans do there," he flicked a couple switches and a screen was turned on, with lots of diagrams and writing on it.

Suddenly, the screen went black.

"What?" the Doctor flicked some more switches in an attempt to retriev the power.

"Doctor," a shape appeared on the monitor, it was speaking to him.

"Doctor," the shape was faint and transparent, but you could see the outline of eyes and a mouth.

"Who are you?" the Doctor spoke to the screen, New Directions were stunned and silent.

And with that, the shape began to sing, high and flowy. It sent shivers down every spine.

The Doctor narrowed his eyes and watched intently until the screen flickered, and both the sound and the face were gone.

"No! Come back!" he yelled, trying to retrieve the haunting creature.

"What was that," Amy asked breathlessly, taking her position by the Doctors side.

"I don't know, I don't know, I don't know," he repeated, his words turning into a frustrated yell at the end.

Whilst the Doctor and Amy franticly pushed buttons, Kurt looked around at his surroundings, and noticed a small black case in the Doctors jacket pocket that he had flung on the chair. Subtly, he removed the item an opened it.

Words began to write themselves onto the page before his widened eyes.

_**We shelter under the surface,**_

_**We are heartless**_

"Doctor!" he squealed, waving the paper in his direction.

"The physic paper of course!" he sped towards Kurt, snatched the paper from his grasp and reading it over and over again.

"Doctor what does it say?" Amy asked.

"We shelter under the surface, we are heartless," he said quietly, tightening his grip on the paper.

"Under the surface? As in underground? Under our school?" Finn questions received no answer as before he knew it, the Doctor sprung into action, shouting commands and orders.

"McKinley high school new Directions, dig out your wellies because we're taking a field trip, down under."

**Please review! **

**Next chapter: The group team together as they try to solve the mysterious singing and the message on the physic paper. And someone takes a liking to the Doctor. **


	4. Chapter 4

**Hi, sorry for the long wait on the update! Jut to clear things up, this takes place after season 2 of glee, Blaine transferred to McKinley and is in New Directions. THERE IS NO FINCHEL. Never has been **

**Doctor Glee**

"No, no, I'm not going down there," Kurt shook his head repeatedly, looking down at his fellow glee clubbers along with the Doctor and Amy.

"Kurt, come on, we all have to group together," Blaine tried to reason with him, holding one of his hands as he stood on the ladder leading down to the sewers. The rest of the teenagers were already down there, although, their mission was put on stand by while Santana, Rachel, and Brittany ran home to change their outfits.

"Hey, you," the Doctor spoke up to Kurt from the darkness, waving his hand about, trying to remember his name, "Ralph Jacobs, are you coming or not, because I'd really like to get going," Kurt looked offended at The Doctor's mix up of two of his idols and continued to shake his head.

"No, I'm sorry Doctor, I'm not going, it stinks and it's dangerous and AH!" he was interrupted by Blaine picking him up, Bridal style, and taking them both down the ladder.

"Blaine! Put me down!" he swatted the curly haired boys chest and kicked his legs about. Blaine just shook his head and looked to the Doctor, "Lead, the way guys," he smiled a little and followed the pair with a protesting Kurt in his arms.

All armed with flash lights and determination, the newly formed group trudged through the sewers, the man in the bow tie and the redhead at the front.

"Doctor?" came a voice from behind the man, he looked back and sighed,"Yeah?" he responded, scanning things as he went along.

"Do you need any help down there at the front?" the familiar whiney voice The Doctor automatically knew was Rachel's. He didn't turn round and just continued walking, "Nope, I'm ok thanks, Rachel,"

The brunette didn't even listen and just pushed her way through the group and walked along side the doctor. She took his arm and smiled up at him.

"Ugh!" he jumped and looked down and the small girl with a look of confusion, "Oh, look, there you are!"

"Yes, I really didn't like the idea of you being at the front, a perfect target for any approaching monsters on your own," se grinned and practically started skipping.

The man just peeled her hands off him and chuckled nervously, "I'm perfectly fine, thank you, besides, I have Am-," he looked around and his face immediately showed panic and worry, "Amy? Amy?" he looked around the group, and only saw blank faces in return, "Has anyone seen Amy?" all heads shook, suddenly Mercedes gasped.

"Oh my God, where's Kurt and Blaine?" by now, everyone was worried and looking around them for any sight of the missing people.

"They were behind me a minute ago!" she added, gripping her hair in worry.

"Doctor, what's going on?" Quinn stepped forward, hands on her hips. The Doctor's jaw dropped, then closed, he raised his eyebrows and shrugged, looking over the heads of all the glee club members.

"I don't know, but I have a very good suggestion tat you may wish to take on board, I think, we, should, run!" he turned quickly and ran down the narrow tunnel, followed by a hoard of screaming teenagers.

"Doctor, what are we running from?" a breathless Finn asked.

"Look behind you, Fann," the Doctor screamed, turning a corner.

Then, as told, Finn slowed down a little to turn his head to what they were all running from. He saw 5 ghostly figures, transparent and white. They had looks of demons on their faces and travelled with most unwarrantable speed. Followed by bolts of lightning, threatening to hit any one of the glee members.

"SHIT!" Finn exclaimed, running even faster.

The haunting melody provided the soundtrack to their death chase, familiar and chilling.

The Doctor ran faster than anyone, knees up and arms flailing. He led them towards a room with a lock on the door, "Every body in!" he yelled, followed by everyone piling into the small, vent like space. It was metal and stunk like, well, sewers weirdly.

"Oh my God, what was that?" Santana wheezed, getting her breath back.

"I don't know, but something tells me they weren't happy," the Doctor looked confused at his scanner and began scanning the door.

"So, where's Kurt, Blaine and Amy?" Mr Schue reminded him, his face automatically dropped, "I don't know," he said simply, then returned to scanning the door.

"My God, it stinks in here," Puck said in disgust.

"We are in a sewer, Noah," Quinn rolled her eyes, bending over to get her breath back, Puck happily watched from behind.

The Doctor's face was pressed against the metal door, listening for a sign of any movement outside. He felt an arm snake through and link around his arm, he looked down to see Rachel, again.

"You were so brave just then, the way you ran and saved us all from danger," she smiled and bit her bottom lip.

"You, ugh," he pointed to her arm and shuddered, "Why don't you um, Mr Schuester," he smiled, looking at the man, "Why don't you tell Racquel,"

"Rachel," she corrected.

"Rachel, why don't you tell Rachel that you'll give her a solo or something?" he noticed the look of anger on his face and he pleaded with him silently.

"Fine, come here Rachel," Rachel left the Doctor's side with a huff, not even listening to the Will promise her a Barbra solo next competition.

"Ok, I'm gonna go out," he whispered, a look of excitement on his face, tinged with worry.

"Be careful," Mercedes warned.

"Oh, I always am" he asked with a smirk.

**Sorry this one is really short, the next one will be longer and the penultimate one **


End file.
